.xlsx to .sdf conversion


I am currently working on a research project pertaining to the Corona Virus. How can I convert a .xlsx file to a .sdf file.

Thank you.

Hi @medicoanas
No idea if this is possible within Knime, but through google I found https://www.spectralcore.com/fullconvert which seems to be able to convert from xlsx to sdf (and some other database formats).
They have a free 30 day trial version, so if it’s a one time action this will do.

Those are fundamentally different file types and structures and contain very different kinds of data.

What information is in the Excel file, and what information are you trying to retain?

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See if this works for you


There seem to be several packages out there dealing biological and chemical data and also KNIME has a strong footing in that community.

There is this R package you might be able to use from KNIME.


Maybe if you provide us with sample data and an idea what result you would want someone might be able to help.

Assuming you’ve only got simple data then this is a fairly trivial task using KNIME and there’s multiple ways to do step 3 below.

The steps you need

  1. Read in the excel file (assuming it’s a simple table)
  2. Use the molecule type cast node to cast the string cell to the appropriate structure cell type. I would guess this is in smiles?
  3. Convert the structure column to mol format
  4. Use the sdf writer

You may not be able to keep everything in your excel file and I’ve assumed your structures are in SMILES format within the excel file.

Only limitation is that the SDF Writer implementaiton KNIME uses ASCII encoding for the SDF.

Here’s an example:



Hello all, I am currently working with an excel file containing over 23,000 anti viral drugs. We have calculated the padel descriptors for our list to curate the list down a bit. The worksheet comprises of ligands represented by the rows and scaled values of padel descriptors represented by the columns. Attached below is a screenshot of the worksheet we are working with. What would be the ideal way of converting this excel worksheet to an .sdf file. Thank you.

Converting this to SDF doesn’t make any sense because SDF is a chemical structure file format and hence it would make sense to have a chemical structure in it. I assume to whatever target programming this goes will expect a chemical structure anyway.

Of course there is always a way. As Sweeb showed but instead just create an empty column as place holder for the structure column, convert that to mol format and in the sdf writer check the box to write empty molecules. But this is a bit non-sensical not knowing more background.


thank you, i shall provide more background pertaining to the question and the files.